Dataset Information

RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root.

ABSTRACT: Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short- (6?h) and long-term (48?h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.

SUBMITTER: Safavi-Rizi V

PROVIDER: S-EPMC6997459 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root.

Safavi-Rizi Vajiheh V Herde Marco M Stöhr Christine C

Scientific reports 20200203 1

Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modul ...[more]

PMID: 32015352

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Project description:BackgroundHigh temperature is one of the major abiotic stresses in tomato and greatly reduces fruit yield and quality. Identifying high-temperature stress-responsive (HSR) genes and breeding heat-tolerant varieties is an effective way to address this issue. However, there are few reports on the fine mapping of heat-tolerance quantitative trait locus (QTL) and the identification of HSR genes in tomato. Here, we applied three heat tolerance-related physiological indexes, namely, relative electrical conductivity (REC), chlorophyll content (CC) and maximum photochemical quantum efficiency (Fv/Fm) of PSII (photosystem II), as well as the phenotypic index, the heat injury index (HII), and conventional QTL analysis combined with QTL-seq technology to comprehensively detect heat-tolerance QTLs in tomato seedlings. In addition, we integrated the QTL mapping results with RNA-seq to identify key HSR genes within the major QTLs.ResultsA total of five major QTLs were detected: qHII-1-1, qHII-1-2, qHII-1-3, qHII-2-1 and qCC-1-5 (qREC-1-3). qHII-1-1, qHII-1-2 and qHII-1-3 were located, respectively, in the intervals of 1.43, 1.17 and 1.19 Mb on chromosome 1, while the interval of qHII-2-1 was located in the intervals of 1.87 Mb on chromosome 2. The locations observed with conventional QTL mapping and QTL-seq were consistent. qCC-1-5 and qREC-1-3 for CC and REC, respectively, were located at the same position by conventional QTL mapping. Although qCC-1-5 was not detected in QTL-seq analysis, its phenotypic variation (16.48%) and positive additive effect (0.22) were the highest among all heat tolerance QTLs. To investigate the genes involved in heat tolerance within the major QTLs in tomato, RNA-seq analysis was performed, and four candidate genes (SlCathB2, SlGST, SlUBC5, and SlARG1) associated with heat tolerance were finally detected within the major QTLs by DEG analysis, qRT-PCR screening and biological function analysis.ConclusionsIn conclusion, this study demonstrated that the combination of conventional QTL mapping, QTL-seq analysis and RNA-seq can rapidly identify candidate genes within major QTLs for a complex trait of interest to replace the fine-mapping process, thus greatly shortening the breeding process and improving breeding efficiency. The results have important applications for the fine mapping and identification of HSR genes and breeding for improved thermotolerance.

Project description:Golden Pompano (Trachinotus blochii) has rapidly developed into the one of the main valuable fish species in Chinese marine aquaculture. Due to its rapid growth, active metabolism, and high oxygen consumption, hypoxia will increase its mortality and cause serious economic losses. We constructed two experimental groups of fish with different degrees of tolerance to hypoxia, used BSR-Seq analysis based on genome and genetic linkage groups to locate SNPs and genes that were related to the differences in hypoxia tolerance. The results showed that hypoxia tolerance SNPs of golden pompano may be jointly determined by multiple linkage groups, especially linkage groups 18 and 22. There were 768 and 348 candidate genes located in the candidate regions of the brain and liver, respectively. These genes were mainly involved in anaerobic energy metabolism, stress response, immune response, waste discharge, and cell death. The prostaglandin-endoperoxide synthase 2 (PTGS2) on LG8, which is involved in the metabolism of arachidonic acid, has a G/A nonsynonymous mutation at position 20641628, and the encoded amino acid was changed from hydrophobic aspartic acid to asparaginate. The specific pathway of the RIG-I-like receptor signaling pathway in the liver may mediate the metabolic system and the immune system, linking glucose metabolism with immune regulation. The death of the hypoxia-intolerant group may be due to the accumulation of lactic acid caused by the activation of anaerobic glycolysis during the early stage of hypoxia stress, and the activation of type I interferon was inhibited, which resulted in decreased immunity. Among the genes involved in the RIG-I-like receptor signaling pathway, the CYLD Lysine 63 Deubiquitinase (CYLD) located on LG16 had a G/T nonsynonymous mutation at position 13629651, and the encoded amino acid was changed from alanine acid to valine. The interferon induced with helicase C domain 1 (Ifih1) located on LG18 has a G/C nonsynonymous mutation at position 16153700, and the encoded hydrophilic glycine was changed to hydrophobic alanine. Our findings suggest these SNPs may assist in the molecular breeding of hypoxia-tolerant golden pompano, and speculate that the balance of glucose and lipid metabolism plays a key role in Trachinotus blochii under acute hypoxia.

Project description:BackgroundRice plants show yellowing, stunting, withering, reduced tillering and utimately low productivity in susceptible varieties under low temperature stress. Comparative transcriptome analysis was performed to identify novel transcripts, gain new insights into different gene expression and pathways involved in cold tolerance in rice.ResultsComparative transcriptome analyses of 5 treatments based on chilling stress exposure revealed more down regulated genes in susceptible and higher up regulated genes in tolerant genotypes. A total of 13930 and 10599 differentially expressed genes (DEGs) were detected in cold susceptible variety (CSV) and cold tolerant variety (CTV), respectively. A continuous increase in DEGs at 6, 12, 24 and 48 h exposure of cold stress was detected in both the genotypes. Gene ontology (GO) analysis revealed 18 CSV and 28 CTV term significantly involved in molecular function, cellular component and biological process. GO classification showed a significant role of transcription regulation, oxygen, lipid binding, catalytic and hydrolase activity for tolerance response. Absence of photosynthesis related genes, storage products like starch and synthesis of other classes of molecules like fatty acids and terpenes during the stress were noticed in susceptible genotype. However, biological regulations, generation of precursor metabolites, signal transduction, photosynthesis, regulation of cellular process, energy and carbohydrate metabolism were seen in tolerant genotype during the stress. KEGG pathway annotation revealed more number of genes regulating different pathways resulting in more tolerant. During early response phase, 24 and 11 DEGs were enriched in CTV and CSV, respectively in energy metabolism pathways. Among the 1583 DEG transcription factors (TF) genes, 69 WRKY, 46 bZIP, 41 NAC, 40 ERF, 31/14 MYB/MYB-related, 22 bHLH, 17 Nin-like 7 HSF and 4C3H were involved during early response phase. Late response phase showed 30 bHLH, 65 NAC, 30 ERF, 26/20 MYB/MYB-related, 11 C3H, 12 HSF, 86 Nin-like, 41 AP2/ERF, 55 bZIP and 98 WRKY members TF genes. The recovery phase included 18 bHLH, 50 NAC, 31 ERF, 24/13 MYB/MYB-related, 4 C3H, 4 HSF, 14 Nin-like, 31 bZIP and 114 WRKY TF genes.ConclusionsTranscriptome analysis of contrasting genotypes for cold tolerance detected the genes, pathways and transcription factors involved in the stress tolerance.

Project description:Waterlogging has increasingly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 waterlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines. BSR-seq was performed to identify differentially expressed genes and SNPs associated with waterlogging tolerance. Upon waterlogging stress, 354 and 1094 genes were differentially expressed in the tolerant and sensitive pools, respectively, compared to untreated controls. When tolerant and sensitive pools were compared, 593 genes were differentially expressed under untreated and 431 genes under waterlogged conditions, of which 122 genes overlapped. To validate the BSR-seq results, the expression levels of six genes were determined by qRT-PCR. The qRT-PCR results were consistent with BSR-seq results. Comparison of allelic polymorphism in mRNA sequences between tolerant and sensitive pools revealed 165 (normal condition) and 128 (waterlogged condition) high-probability SNPs. We found 18 overlapping SNPs with genomic positions mapped. Eighteen SNPs were contained in 18 genes, and eight and nine of 18 genes were responsive to waterlogging stress in tolerant and sensitive lines, respectively. Six alleles of the 18 originated from tolerant pool were significantly up-regulated under waterlogging, but not those from sensitive pool. Importantly, one allele (GRMZM2G055704) of the six genes was mapped between umc1619 and umc1948 on chromosome 1 where a QTL associated with waterlogging tolerance was identified in a previous research, strongly indicating that GRMZM2G055704 is a candidate gene responsive to waterlogging. Our research contributes to the knowledge of the molecular mechanism for waterlogging tolerance in maize.

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RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root.

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RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root.

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